MRG: Merge branch 'main' into features/melinatorcosiupdates

zoglauer · Dec 1, 2023 · 9190634 · 9190634
2 parents 6ab384d + 27f07bd
commit 9190634
Show file tree

Hide file tree

Showing 30 changed files with 431 additions and 379 deletions.
diff --git a/Makefile b/Makefile
@@ -13,17 +13,17 @@
 
 MAKE += -s
 
-SHELL=/bin/bash
+SHELL	:=/bin/bash
 
 # Basic directories
-TOP	= $(shell pwd)
-SR	= $(TOP)/src
-IN	= $(TOP)/include
-LB	= $(TOP)/lib
-BN	= $(TOP)/bin
-HT	= $(TOP)/doc/html
-CT	= $(TOP)/cint
-CF	= $(TOP)/config
+TOP	:= $(shell pwd)
+SR	:= $(TOP)/src
+IN	:= $(TOP)/include
+LB	:= $(TOP)/lib
+BN	:= $(TOP)/bin
+HT	:= $(TOP)/doc/html
+CT	:= $(TOP)/cint
+CF	:= $(TOP)/config
 
 #------------------------------------------------------------------------------
 # Included options (result of ./configure)
@@ -54,7 +54,7 @@ LDFLAGS     += -L$(LB)
 #------------------------------------------------------------------------------
 # Commands:
 
-CMD=
+CMD :=
 
 #.NOPARALLEL:
 .EXPORT_ALL_VARIABLES: all copy miw geo geolib
@@ -71,8 +71,8 @@ only: info glo geo spe rev siv res mim evi rea fre add cos
 #------------------------------------------------------------------------------
 # Version check:
 
-ROOTVERSIONOK   = $(shell bash $(CF)/configure_rootversiontest )
-GEANT4VERSIONOK = $(shell bash $(CF)/configure_geant4versiontest )
+ROOTVERSIONOK   := $(shell bash $(CF)/configure_rootversiontest )
+GEANT4VERSIONOK := $(shell bash $(CF)/configure_geant4versiontest )
 
 
 #------------------------------------------------------------------------------

diff --git a/bin/dcosima b/bin/dcosima
@@ -46,7 +46,7 @@ commandhelp() {
   echo "  --source=[filename]: The source file"
   echo "  --continue=[name]: Continue a simulation run with the given name (ignores --source & --prefix)"
   echo "  --delay=[number] Time between searches for free slots -- the longer the delay time the lower the priority of this instance (default: 10 seconds)"
-  echo "  --zip: Compress the output files."
+  echo "  --unzip: Do not compress the output files (gzip'ing them is the default)."
   echo "  --log: Create a log file of what is started where"
   echo "  --help: Show this help."
   echo ""
@@ -80,7 +80,7 @@ SOURCE=""
 SOURCEFILENAME=""
 INSTANCES="1"
 PREFIX=""
-ZIP="FALSE"
+ZIP="TRUE"
 CONTINUE=""
 LOG="FALSE"
 LOGFILE=""
@@ -109,6 +109,8 @@ for C in "${CMD[@]}"; do
     CONTINUE=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-z* ]]; then
     ZIP="TRUE"
+  elif [[ ${C} == *-u* ]]; then
+    ZIP="FALSE"
   elif [[ ${C} == *-d* ]]; then
     DELAY=`echo ${C} | awk -F"=" '{ print $2 }'`
   elif [[ ${C} == *-l* ]]; then
@@ -234,6 +236,12 @@ if [[ ${LOG} == "TRUE" ]]; then
   echo " * Logging output to file: ${LOGFILE}"
 fi
 
+if [[ ${ZIP} == "TRUE" ]]; then
+  echo " * Gzip'ing output"
+else
+  echo " * Not gzip'ing output"
+fi
+
 if [[ ${INSTANCES} -gt 0 ]]; then
   echo " * Simulations instances: ${INSTANCES}"
 else
@@ -674,7 +682,11 @@ if [[ ${LAUNCHED} -gt 0 ]]; then
   echo " " >> ${ConcatFileName}
 
   for (( i=1; i <= ${INSTANCES}; i+=1 )); do
-    echo "IN ${Base}.p1.inc${i}.id1.sim" >> ${ConcatFileName}
+    if [[ "${ZIP}" == "TRUE" ]]; then
+      echo "IN ${Base}.p1.inc${i}.id1.sim.gz" >> ${ConcatFileName}
+    else
+      echo "IN ${Base}.p1.inc${i}.id1.sim" >> ${ConcatFileName}
+    fi
   done
 
   echo "EN" >> ${ConcatFileName}

diff --git a/bin/dcosima-runinstance b/bin/dcosima-runinstance
@@ -265,7 +265,7 @@ OUT="/dev/null"
 if [[ ${LOGFILE} != "" ]]; then
   OUT="Sim.inc${INSTANCEID}.log"
 fi
-ssh -i ${HOME}/.ssh/dmegalib_rsa -p ${REMOTEPORT} ${REMOTEUSER}@${REMOTEHOST} ". ~/.dmegalib.bashrc; cd ${MASTERDIR}/${RUNDIR}; nohup nice -n ${NICELEVEL} cosima -p 1 -f ${INSTANCEID} -t ${RUNDIR} -v 0 -s ${SEED} `if [[ ${ZIP} == TRUE ]]; then echo "-z"; fi` ${SOURCEFILE} > ${OUT} 2>&1 &"
+ssh -i ${HOME}/.ssh/dmegalib_rsa -p ${REMOTEPORT} ${REMOTEUSER}@${REMOTEHOST} ". ~/.dmegalib.bashrc; cd ${MASTERDIR}/${RUNDIR}; nohup nice -n ${NICELEVEL} cosima -p 1 -f ${INSTANCEID} -t ${RUNDIR} -v 0 -s ${SEED} `if [[ ${ZIP} == FALSE ]]; then echo "-u"; fi` ${SOURCEFILE} > ${OUT} 2>&1 &"
 if [ "$?" != "0" ]; then
   echo "ERROR: Failed to start the simulations" | ${LOGGING}
   exit 1

diff --git a/bin/dmegalib-setup b/bin/dmegalib-setup
@@ -18,7 +18,7 @@ commandhelp() {
   echo ""
   echo "";
   echo "Example: "
-  echo "  dmegalib-setup --machines=thebe,despina,carpo,sinope,carme,royal,leda,elara,cosi-ccu";
+  echo "  dmegalib-setup --machines=thebe,despina,carpo,dione,sinope,carme,leda,royal";
   echo "";
 }
 

diff --git a/config/Makefile.linuxclang b/config/Makefile.linuxclang
@@ -9,23 +9,23 @@
 #----------------------------------------------------------------
 
 
-CMODE         = "Linux with clang compiler"
-DLL           = so
+CMODE         := "Linux with clang compiler"
+DLL           := so
 
 # Basic flags generated by ROOT
-ROOTCFLAGS    = $(shell root-config --cflags)
-ROOTLIBS      = $(shell root-config --libs)
-ROOTGLIBS     = $(shell root-config --glibs)
+ROOTCFLAGS    := $(shell root-config --cflags)
+ROOTLIBS      := $(shell root-config --libs)
+ROOTGLIBS     := $(shell root-config --glibs)
 
 # Compiler & linker options:
-CXX           = clang++
-CXXFLAGS      = $(OPT) -std=c++0x -Wall -Wno-deprecated -fPIC -Wno-overloaded-virtual -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___LINUX___ -D___CLING___
-DEFINES       = -UHARDWARE
-LD            = clang++
-LDFLAGS       = $(OPT) -D___LINUX___
-SOFLAGS       = -shared  
-LIBS          = $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
-GLIBS         = $(ROOTGLIBS) 
-DEPFLAGS      = -MD -MF
+CXX           := clang++
+CXXFLAGS      := $(OPT) -std=c++0x -Wall -Wno-deprecated -fPIC -Wno-overloaded-virtual -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___LINUX___ -D___CLING___
+DEFINES       := -UHARDWARE
+LD            := clang++
+LDFLAGS       := $(OPT) -D___LINUX___
+SOFLAGS       := -shared  
+LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
+GLIBS         := $(ROOTGLIBS) 
+DEPFLAGS      := -MD -MF
 
-LINK          = ln -s -f
+LINK          := ln -s -f
diff --git a/config/Makefile.linuxgcc b/config/Makefile.linuxgcc
@@ -9,30 +9,30 @@
 #----------------------------------------------------------------
 
 
-CMODE         = "Linux with gcc utilizing C++14"
-DLL           = so
+CMODE         := "Linux with gcc utilizing C++14"
+DLL           := so
 
 # Basic flags generated by ROOT
-ROOTCFLAGS    = $(shell root-config --cflags)
-ROOTLIBS      = $(shell root-config --libs)
-ROOTGLIBS     = $(shell root-config --glibs)
+ROOTCFLAGS    := $(shell root-config --cflags)
+ROOTLIBS      := $(shell root-config --libs)
+ROOTGLIBS     := $(shell root-config --glibs)
 
 # Compiler & linker options:
-CXX           = g++
-CXXFLAGS      = $(OPT) -std=c++14 -Wall -Wno-deprecated -fPIC -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___LINUX___ -D___CLING___
-DEFINES       = -UHARDWARE
-LD            = g++
-LDFLAGS       = $(OPT) -D___LINUX___
-SOFLAGS       = -shared  
-LIBS          = $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
-GLIBS         = $(ROOTGLIBS) 
-DEPFLAGS      = -MM
+CXX           := g++
+CXXFLAGS      := $(OPT) -std=c++14 -Wall -Wno-deprecated -fPIC -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___LINUX___ -D___CLING___
+DEFINES       := -UHARDWARE
+LD            := g++
+LDFLAGS       := $(OPT) -D___LINUX___
+SOFLAGS       := -shared  
+LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
+GLIBS         := $(ROOTGLIBS) 
+DEPFLAGS      := -MM
 
-LINK          = ln -s -f
+LINK          := ln -s -f
 
 # HEASoft
-HEACFLAGS     = 
-HEALIBS       =
+HEACFLAGS     := 
+HEALIBS       :=
 ifneq ("$(wildcard $(LHEASOFT)/include/fitsio.h)", "")
 	HEACFLAGS += -I$(LHEASOFT)/include
 	HEALIBS += -L$(LHEASOFT)/lib 

diff --git a/config/Makefile.linuxicc b/config/Makefile.linuxicc
@@ -9,23 +9,23 @@
 #----------------------------------------------------------------
 
 
-CMODE         = "Linux with icc compiler"
-DLL           = so
+CMODE         := "Linux with icc compiler"
+DLL           := so
 
 # Basic flags generated by ROOT
-ROOTCFLAGS    = $(shell root-config --cflags)
-ROOTLIBS      = $(shell root-config --libs)
-ROOTGLIBS     = $(shell root-config --glibs)
+ROOTCFLAGS    := $(shell root-config --cflags)
+ROOTLIBS      := $(shell root-config --libs)
+ROOTGLIBS     := $(shell root-config --glibs)
 
 # Compiler & linker options:
-CXX           = icc
-CXXFLAGS      = $(OPT) -fPIC -wd1572 -wd1125 -wd654 -wd191 -wd1224 -wd1476 -wd913 -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___LINUX___ -D___CLING___
-DEFINES       = -UHARDWARE
-LD            = icc
-LDFLAGS       = $(OPT) -D___LINUX___
-SOFLAGS       = -shared  
-LIBS          = $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
-GLIBS         = $(ROOTGLIBS) 
-DEPFLAGS      = -M
+CXX           := icc
+CXXFLAGS      := $(OPT) -fPIC -wd1572 -wd1125 -wd654 -wd191 -wd1224 -wd1476 -wd913 -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___LINUX___ -D___CLING___
+DEFINES       := -UHARDWARE
+LD            := icc
+LDFLAGS       := $(OPT) -D___LINUX___
+SOFLAGS       := -shared  
+LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
+GLIBS         := $(ROOTGLIBS) 
+DEPFLAGS      := -M
 
-LINK          = ln -s -f
+LINK          := ln -s -f
diff --git a/config/Makefile.macosx b/config/Makefile.macosx
@@ -9,31 +9,31 @@
 #----------------------------------------------------------------
 
 
-CMODE         = "MacOSX with clang compiler"
-ARCH          = macosx
-DLL           = so
+CMODE         := "MacOSX with clang compiler"
+ARCH          := macosx
+DLL           := so
 
 # Basic flags generated by ROOT
-ROOTCFLAGS    = $(shell root-config --cflags)
-ROOTLIBS      = $(shell root-config --libs)
-ROOTGLIBS     = $(shell root-config --glibs)
+ROOTCFLAGS    := $(shell root-config --cflags)
+ROOTLIBS      := $(shell root-config --libs)
+ROOTGLIBS     := $(shell root-config --glibs)
 
 # Compiler & linker options:
-CXX           = c++
-CXXFLAGS      = $(OPT) -std=c++14 -pipe -Wall -fPIC -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___MACOSX___ -D___CLING___ -Wno-unused-but-set-variable -Wno-overloaded-virtual -Wno-tautological-undefined-compare -Wno-deprecated-declarations
-DEFINES       = -UHARDWARE
-LD            = c++
-LDFLAGS       = $(OPT) -Xlinker -bind_at_load -flat_namespace -D___MACOSX___
-SOFLAGS       = -dynamiclib -flat_namespace -undefined suppress 
-LIBS          = $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
-GLIBS         = $(ROOTGLIBS) 
-DEPFLAGS      = -M
-
-LINK          = ln -s -f
+CXX           := c++
+CXXFLAGS      := $(OPT) -std=c++14 -pipe -Wall -fPIC -D_REENTRANT -I$(IN) -I$(CT) -I. $(ROOTCFLAGS) -D___MACOSX___ -D___CLING___ -Wno-unused-but-set-variable -Wno-overloaded-virtual -Wno-tautological-undefined-compare -Wno-deprecated-declarations
+DEFINES       := -UHARDWARE
+LD            := c++
+LDFLAGS       := $(OPT) -Xlinker -bind_at_load -flat_namespace -D___MACOSX___
+SOFLAGS       := -dynamiclib -flat_namespace -undefined suppress 
+LIBS          := $(ROOTLIBS) -lpthread -lThread -lMinuit -lGeom -lSpectrum -lTMVA
+GLIBS         := $(ROOTGLIBS) 
+DEPFLAGS      := -M
+
+LINK          := ln -s -f
 
 # HEASoft
-HEACFLAGS     =
-HEALIBS       =
+HEACFLAGS     :=
+HEALIBS       :=
 ifneq ("$(wildcard $(LHEASOFT)/include/fitsio.h)", "")
         HEACFLAGS += -I$(LHEASOFT)/include
         HEALIBS += -L$(LHEASOFT)/lib

diff --git a/configure b/configure
@@ -515,9 +515,9 @@ echo "# Section A: Additional libraries" >> config/Makefile.options
 echo "# " >> config/Makefile.options
 echo "# Important: Don't modify this sections by yourself " >> config/Makefile.options
 echo " " >> config/Makefile.options
-echo "GEANT4INSTALLED  = ${Geant4Found}" >> config/Makefile.options
-echo "HEASOFTINSTALLED = ${FitsIOFound}" >> config/Makefile.options
-echo "MPIINSTALLED = ${MPIFound}" >> config/Makefile.options
+echo "GEANT4INSTALLED  := ${Geant4Found}" >> config/Makefile.options
+echo "HEASOFTINSTALLED := ${FitsIOFound}" >> config/Makefile.options
+echo "MPIINSTALLED     := ${MPIFound}" >> config/Makefile.options
 echo " " >> config/Makefile.options
 
 echo "# " >> config/Makefile.options
@@ -538,7 +538,7 @@ if [[ ${ARCH} == linux ]]; then
 fi
 echo "Please see the file config/Makefile.options for more optimization options for the Intel and GNU compiler"
 echo "" >> config/Makefile.options
-echo "OPT = ${OPTIONS}" >> config/Makefile.options
+echo "OPT := ${OPTIONS}" >> config/Makefile.options
 if ( [ $Geant4Found -eq 0 ] ); then 
     echo "$G4DEBUG" >> config/Makefile.options
 fi
@@ -551,10 +551,10 @@ echo "#            If you have anything else, set it in Makefile.user " >> confi
 echo "# " >> config/Makefile.options
 echo "" >> config/Makefile.options
 if ( [ $Geant4OpenGLFound -eq 0 ] ); then 
-    echo "G4VIS_USE_OPENGLX=1" >> config/Makefile.options
+    echo "G4VIS_USE_OPENGLX  := 1" >> config/Makefile.options
 fi
 if ( [ $Geant4DawnFileFound -eq 0 ] ); then 
-    echo "G4VIS_USE_DAWNFILE=1" >> config/Makefile.options
+    echo "G4VIS_USE_DAWNFILE := 1" >> config/Makefile.options
 fi
 echo "" >> config/Makefile.options
 

diff --git a/resource/examples/advanced/Atmosphere/make_all.sh b/resource/examples/advanced/Atmosphere/make_all.sh
@@ -1,6 +1,6 @@
 
 
 for P in `ls *.cxx`; do
-  make -f ${MEGALIB}/resource/standalone/Makefile.standalone PRG=${P}
+  make -f ${MEGALIB}/resource/standalone/Makefile.StandAlone PRG=${P}
 done
 
diff --git a/resource/examples/advanced/Pipeline/SimulateSources.sh b/resource/examples/advanced/Pipeline/SimulateSources.sh
@@ -32,7 +32,7 @@ PointSourceContinuumPolarizedTemplate=${MEGALIB}/resource/examples/advanced/Pipe
 
 
 THREADS=1
-NCPUS=`cat /proc/cpuinfo | grep "processor" | wc -l`
+NCPUS=`grep ^cpu\\scores /proc/cpuinfo | uniq |  awk '{print $4}'`
 
 # Create the directory where to store the simulation file
 if [ ! -d "${PointSourceDir}" ]; then

diff --git a/src/addon/Makefile b/src/addon/Makefile
@@ -15,7 +15,7 @@
 # Definitions:
 #
 
-PRGSX = \
+PRGSX := \
 	$(BN)/SensitivityOptimizer \
 	$(BN)/Mask \
 	$(BN)/ConvertMGeant \
@@ -37,18 +37,18 @@ PRGSX = \
 	$(BN)/IsotopeFileSplitter \
 	$(BN)/VariableSourceDetector \
 
-FITS = \
+FITS := \
 	$(BN)/TraFitsConverter \
 	$(BN)/ConvertMGGPOD \
 	$(BN)/ResponseToXSPEC \
 
-MPI = $(BN)/bundler
+MPI := $(BN)/bundler
 
 
 
-MLIBS = -L$(LB) -lMimrecGui -lMimrec -lRevanGui -lRevan -lSivanGui -lSivan -lSpectralyzeGui -lSpectralyze -lGeomegaGui -lGeomega -lCommonMisc -lCommonGui  
+MLIBS := -L$(LB) -lMimrecGui -lMimrec -lRevanGui -lRevan -lSivanGui -lSivan -lSpectralyzeGui -lSpectralyze -lGeomegaGui -lGeomega -lCommonMisc -lCommonGui  
 
-EVERYTHING = $(PRGSX) $(FITS)
+EVERYTHING := $(PRGSX) $(FITS)
 
 #----------------------------------------------------------------
 # Commands: